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R.C. Gupta
Professor and Head
Dept. of Biochemistry
National Institute of Medical Sciences
Jaipur, India
Enzymes
A vast multitude of chemical reactions
occur in living organisms
It is these reactions that keep the
organism going
These reactions would occur at extremely
low velocities in the absence of catalysts
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Common catalysts used in non-living
systems are:
Acids Alkalis Metals
These are not suitable for living
organisms because of their:
Toxicity Lack of specificity
Biological catalysts should be:
Safe (non-toxic)
Specific (generally catalyzing
one reaction only)
Capable of adjusting their
catalytic activity
All these properties are present in
enzymes
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Enzymes were first discovered in
yeast (enzyme means ‘in yeast’)
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Chemically, all enzymes were found to be
proteins
They could catalyze reactions outside
the living organisms also
They were later found in other living
organisms as well
Definition
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But this definition is not entirely correct
Enzymes are protein catalysts that catalyse
chemical reactions in biological systems
Some RNA molecules (ribozymes) have
been found to catalyze some reactions
The reactant on which the enzyme acts is
known as the substrate of the enzyme
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Substrate Product
Enzyme
The enzyme converts the substrate into a
product or products
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If an enzyme catalyses a number of
reactions, it will be impossible to
regulate individual reactions
Enzyme specificity
However, the enzymes are highly
specific
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Generally, one enzymes catalyses only
one reaction
This is of crucial importance for
regulation of metabolic pathways
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Enzyme specificity may have
the following orders:
Group specificity
Substrate specificity
Stereo-specificity
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Group specificity
Enzyme is specific for a bond but not
for the actual substrate
Group-specific or bond-specific
enzymes are commonly present in
digestive secretions
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For example, pepsin is specific for
peptide bond but not for any protein
Thus, a large variety of dietary proteins
can be digested by the same enzyme
Trypsin, chymotrypsin, nucleases, lipases
and glycosidases are other examples
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Some group-specific enzymes have a
slightly higher degree of specificity
For example, aminopeptidase
hydrolyses only N-terminal peptide bond
Carboxypeptidase hydrolyses only the
C-terminal peptide bond
Endopeptidases hydrolyse the internal
peptide bonds only
H2N–Phe–Ala–Ser–Cys–Gly–Asp–Arg–Val–Leu–Glu–COOH
Amino-
peptidase
Endo-
peptidase
Carboxy-
peptidase
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Most enzymes are specific for a chemical
bond/group as well as the substrate
For example, glucokinase and fructokinase
are substrate-specific enzymes
They transfer a phosphate group from ATP
to one specific substrate
Substrate specificity
Glucose Glucose-6-Phosphate
Glucokinase
ATP ADP
Fructose Fructose-1-Phosphate
Fructokinase
ATP ADP
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Stereo-specificity
Many biomolecules exhibit stereo-
isomerism
Examples are carbohydrates and
amino acids
Enzymes acting on these are specific
for one stereo-isomer
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Mammalian enzymes acting on carbo-
hydrates are generally specific for
D-isomers
Those acting on amino acids are
generally specific for L-isomers
Exceptions are racemases which
inter-convert the D- and L-isomers
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COOH
I
H2N – C – H
I
CH3
COOH
I
H – C – NH2
I
CH3
Alanine
racemase
L-Alanine D-Alanine
Stereospecificity – An exception
Some enzymes require a non-protein
substance for their catalytic activity
If the non-protein substance is
organic, it is known as a coenzyme
If the non-protein substance is
inorganic, it is known as a cofactor
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Coenzymes and cofactors
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The coenzyme or the
cofactor may be:
An integral part of the enzyme
or
Its presence may be required
during the reaction
The protein portion of an enzyme that
requires a coenzyme is called apoenzyme
Apoenzyme + Coenzyme → Holoenzyme
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Apoenzyme combines with coenzyme to form
the active holoenzyme
COENZYME
APOENZYME HOLOENZYME
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The coenzymes generally contain vitamins
of B-complex family
Some are converted into coenzymes e.g.
thiamin, riboflavin, niacin, pantothenic acid,
pyridoxine, folic acid and vitamin B12
Some act as coenzymes by themselves
e.g. biotin
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Oxidation-reduction
Transamination
Phosphorylation
Coenzymes are generally required
in group transfer reactions e.g.
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Coenzymes can be divided into
two groups:
Coenzymes
involved
in transfer of
hydrogen
Coenzymes
involved in transfer
of groups other
than hydrogen
Coenzymes
involved in
transfer of
hydrogen:
Flavin mononucleotide (FMN)
Flavin adenine dinucleotide (FAD)
Nicotinamide adenine dinucleotide
(NAD+)
Nicotinamide adenine dinucleotide
phosphate (NADP+)
Lipoic acid
Coenzyme Q
Coenzymes
involved in
transfer of
groups
other than
hydrogen:
Thiamin pyrophosphate (TPP)
Coenzyme A (Co A)
Pyridoxal phosphate (PLP)
Tetrahydrofolate (H4- Folate)
Cobamides (B12- Coenzymes)
Lipoic acid
Biotin
ATP & similar nucleotides
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Role of coenzymes
The enzyme acts upon its substrate, and
converts it into a product
Coenzyme acts as a co-substrate or a second
substrate in the group transfer reactions
The coenzyme either donates or accepts
the group that is being transferred
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In the second reaction, the coenzyme NAD+ acts
a second substrate and accepts the hydrogen
atoms
In the first reaction, the coenzyme ATP acts as
a second substrate and donates a phosphate
group
CH2‒OH
CH2‒OH
CH‒OH
Glycerol
CH2‒OH
CH2‒O‒
CH‒OH
CH2‒OH
CH2‒O‒
C = O
ATP
Glycerol
kinase
ADP
Glycerol-3-
phosphate
Dihydroxy-
acetone
phosphate
Glycerol-3-
phosphate
dehydrogenase
NAD+ NADH
+ H+
The chemical change in the coenzyme is
opposite to that in the substrate
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Thus, they act only as carriers, and regain their
original form at the end of the reaction
Pyridoxal phosphate, for example, acts as a
carrier of amino group in transamination
Some coenzymes accept a chemical group from
one substrate and donate it to another
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Aspartate Glutamate
Oxaloacetate a-Ketoglutarate
Pyridoxal phosphate
Pyridoxamine phosphate
Glutamate oxaloacetate
transaminase (GOT)
Pyridoxal phosphate first accepts the amino
group from aspartate, and is converted into
pyridoxamine phosphate
Pyridoxamine phosphate then transfers the
amino group to a-ketoglutarate, and is
converted into pyridoxal phosphate
In the coupled reaction, aspartate is converted
into oxaloacetate, and a-ketoglutarate is
converted into glutamate
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Aspartate + a-Ketoglutarate Oxaloacetate + Glutamate
GOT
PLP
Though pyridoxal phosphate is a reactant,
the reaction is usually shown as:
The coenzyme goes back to its original
form at the end of the reaction
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Sometimes, the change in the coenzyme is
more important than that in the substrate
In glycolysis, glucose is converted into
pyruvate, and NAD+ is reduced in one
reaction
Reduced NAD+ transfers its hydrogen atoms
to oxygen, and NAD+ is regenerated
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Here, regeneration of NAD+ is more important for
continuation of glycolysis
One more reaction occurs in which pyruvate is
reduced to lactate, and NADH is oxidised to NAD+
If the conditions are anaerobic, NAD+ cannot be
regenerated due to lack of oxygen
NAD+
NADH+H+
Glucose
↓
↓
Glyceraldehyde-3-P 1,3-Biphosphoglycerate
↓
↓
↓
↓
Lactate (Anaerobic) Pyruvate (Aerobic)
Enzyme nomenclature and classification
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The nomenclature of enzymes has undergone
many changes over the years
The names assigned to enzymes in the
beginning were very vague and uninformative
Some of the early names are pepsin,
ptylin, zymase etc
These indicate neither the substrates nor the
type of reaction catalyzed by the enzyme
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Later on, a slightly more informative nomen-
clature was adopted
Suffix -ase was added to the name of
the substrate e.g. lipase, protease etc
Still the type of reaction catalyzed by the
enzyme remained unclear
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Nomenclature was modified further, to include
the name of the substrate followed by the
type of reaction ending with -ase
This resulted in names like lactate dehydro-
genase, pyruvate carboxylase, glutamate
decarboxylase etc
Even these names do not give complete
information, for example whether a coenzyme
is required or a byproduct is formed
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To make the names of enzymes informative and
unambiguous, International Union of Biochemistry
(IUB) formed an Enzyme Commission
The enzyme commission proposed a method of
nomenclature and classification of enzymes
which is applicable to all living organisms
According to IUB system:
• The enzymes have been divided into six
classes (numbered 1 - 6)
• Each class is divided into subclasses
• Subclasses are divided into
subsubclasses
• Subsubclasses are divided into
individual enzymes
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Nomenclature
The name of the enzyme has two parts
The first part includes the name(s) of the
substrate(s) including substrate (coenzyme)
The second part includes the type of
reaction ending with -ase
If any additional information is to be given,
it is put in parenthesis at the end
For example, the enzyme having the trivial
name glutamate dehydrogenase catalyzes
the following reaction:
L-Glutamate + NAD(P)+ + H2 O →
a-Ketoglutarate + NAD(P)H + H+ + NH3
According to IUB system, this enzyme is
known as L-Glutamate: NAD(P) oxido-
reductase (deaminating)
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The amino group of L-glutamate is released as
ammonia
NAD+ or NADP+ is required as a co-substrate
This enzyme acts on L-glutamate
The IUB name shows that:
Type of reaction is oxidoreduction i.e. L-glutamate is
oxidised and the co-substrate is reduced
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Moreover, each enzyme has been given
a code number consisting of four digits:
First digit shows the number of the
class
Second digit shows the number of the
subclass
Third digit shows the number of the
subsubclass
Fourth digit shows the number of the
enzyme
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The code number of L-glutamate: NAD(P)
oxidoreductase (deaminating) is EC 1.4.1.3
This shows that is it the third enzyme of
subsubclass 1 of subclass 4 of class 1
EC is the acronym for Enzyme Commission
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The enzymes are
divided into six
classes in IUB
classification:
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
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Oxidoreductases
These are the enzymes that catalyze
oxidation-reduction reactions
One of the substrates is oxidised
and the other is reduced
Different subclasses act on
different chemical groups
Groups undergoing the reaction include
–CH=CH–, >CH–OH, >C=O, >CH–NH2 etc
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Examples of oxidoreductases are:
Glutamate dehydrogenase
Lactate dehydrogenase
Malate dehydrogenase
Glycerol-3-phosphate dehydrogenase
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Transferases
These enzymes transfer a group other than
hydrogen from one substrate to another
Such groups include methyl group, amino
group, phosphate group, acyl group,
glycosyl group etc
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Examples of transferases are:
Hexokinase
Glucokinase
Glutamate oxaloacetate transaminase
Ornithine carbamoyl transferase
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Hydrolases
These enzymes hydrolyse various bonds
such as peptide, ester, glycosidic bonds etc
They are commonly found in the digestive
secretions and lysosomes
They hydrolyse carbohydrates, lipids,
proteins etc
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Examples of
hydrolases are:
Amylase
Lipase
Pepsin
Ribonuclease
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Lyases
These enzymes remove chemical
groups from substrates by
mechanisms other than hydrolysis
The groups removed may be water,
amino group, carboxyl group etc
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Examples of
lyases are:
Aldolase
Enolase
Fumarase
Isomerases
These enzymes catalyse inter-
conversion of isomers of compound
Substrates include aldose-ketose
isomers, stereo-isomers etc
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Examples of isomerases are:
Alanine racemase
Triose phosphate isomerase
Phosphohexose isomerase
Ribose-5-phosphate
ketoisomerase
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Ligases
These enzymes ligate or bind two
substrates together
Binding occurs by a covalent bond
A source of energy is required e.g. a
high-energy phosphate
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Examples of ligases are:
Glutamine synthetase
Squalene synthetase
Acetyl CoA carboxylase
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At temperatures above absolute zero (– 273°C),
molecules are in constant motion because of
their kinetic energy
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A chemical reaction occurs when molecules of
reactants collide with each other in the correct
orientation (kinetic theory of reaction)
Mechanism of action of enzymes
The greater the frequency of collisions
between the reactant molecules, the greater
will be the rate of reaction
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The frequency of collisions can be increased
by raising the temperature
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Rise in temperature
would increase:
Molecular motion
Frequency of collisions
Rate of reaction
Energy input required to reach the critical
level is known as the energy of activation
Energy level of reactants has to be raised
to a critical level for the reaction to occur
In living organisms, the enzymes provide
an alternate pathway for the reaction
Enzymes lower the energy of activation
The option of raising temperature is
not available in living organisms
The enzyme molecules are much larger than
their substrates
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Enzyme-substrate interaction
The substrate binds to this site forming an
enzyme-substrate (ES) complex
An enzyme possesses a specific binding site
for its substrate(s) known as the substrate site
Substrates
bind to enzyme
Bond is
formed
Product is
released
The binding may bring two substrates in
close proximity (bond-forming distance) in
the correct orientation so that a bond is
formed between the two
The binding of a substrate to the enzyme
many induce a strain in the substrate
As a result, a bond is broken in the
substrate
The substrate is split into two or more
products which are released
Enzyme ‒
Substrate ‒
Products ‒
Substrate binds
to enzyme
A strain occurs in the
substrate; a bond is
broken
Substrate splits into
products which are
released
On binding of two substrates to the enzyme,
a chemical group may be transferred from
one substrate to another
The catalytic action of the enzyme may
be exerted by:
Cofactors
Coenzymes
Some amino acid residues in the
substrate site
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In the reaction catalysed by carbonic anhydrase,
the cofactor (zinc) catalyses
the reaction
‒ Zn++
H+ + HCO3
‒
H2O
‒ Zn++
...‒O + H+
H
I
CO2
‒ Zn++
+ O‒C‒O‒ + H+
H
I
II
O
‒ Zn++
...O‒C‒O
H
I
II
O
H
I
‒ Zn++
...O + C = O...H+
H
I
II
O
‒
In transamination reactions, the coenzyme
(pyridoxal phosphate) is involved in catalysis
Pyridoxal phosphate is present at the
substrate site
It accepts an amino group from an amino
acid, and then donates it to a keto acid
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Coenzyme
Common amino acid residues in the substrate
site are serine, histidine, cysteine, aspartate etc
Serine proteases are proteolytic enzymes in
which serine residues catalyse hydrolysis
Examples of serine proteases are trypsin,
chymotrypsin, thrombin etc
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The first model was
proposed by Emil
Fischer
Also known as
rigid template
model
A different model
was later proposed
by Koshland
Also known as
induced fit
model
Models of enzyme conformation
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Fischer’s
model
Conformation of enzymes
very rigid
Lock and key type of
complementarity between
substrate and enzyme
Complementarity responsible
for specificity of enzymes
Lock
Key
Fischer’s model
Fischer’s model did not agree with
certain experimental findings
obtained later
Conformation of enzyme was found to
change when it combined with its substrate
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Before substrate binding After substrate binding
Substrate Enzyme
Koshland’s model conforms to known findings
In the absence of substrate, complementarity
between enzyme and substrate is not
apparent
Approach of substrate induces change in
conformation of the enzyme
The substrate site becomes
complementary to the substrate
The substrate binds to the enzyme, and is
converted into the product
Release of the product restores the
enzyme to its original conformation
Change in conformation of the enzyme
produces ‘induced fit’
Koshland’s model
Allosteric enzymes
Some enzymes possess a site, in addition to
the substrate site, known as the allosteric site
Binding of an allosteric molecule to allosteric
site changes the conformation of the enzyme
Enzymes having allosteric site are termed as
allosteric enzymes
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Allosteric regulator
Allosteric modifier
Allosteric effector
The allosteric molecule
is also known as:
Some allosteric molecules:
Facilitate the conformational change
required for substrate binding
They are known as allosteric activators
(positive modifiers)
An example is N-acetylglutamate which
activates carbamoyl phosphate synthetase
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Enzyme
Substrate site
Allosteric site
Substrate
Allosteric
activator
Allosteric activator
binds to enzyme;
substrate site
changes
Substrate can
now bind to
substrate site
Some allosteric regulators:
Prevent the conformational change required
for the binding of the substrate
Such regulators are known as allosteric
inhibitors (negative modifiers)
An example is glucose-6-phosphate which
inhibits hexokinase
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Enzymes subject to allosteric inhibition are
usually present at the start of long pathways
The allosteric enzyme regulates the rate of
formation of the product
The allosteric inhibitor is generally the product
of the pathway
If the product is not being utilised, it
will accumulate
It inhibits the allosteric enzyme, and further
synthesis of the product ceases
When the product is used up, the allosteric
enzyme becomes free and active again
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E1 is an allosteric enzyme,
and P is its allosteric inhibitor
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S I1 I2 I3 I4 P
E1 E2 E3 E4 E5
Θ
Factors affecting the rates of
enzyme-catalysed reactions
Enzyme concentration
Substrate concentration
Coenzyme concentration
Temperature
pH
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Enzyme concentration
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An enzyme catalyses a reaction by
forming enzyme-substrate complex
Enzyme-substrate complex dissociates
into the enzyme and the product
E + S ↔ E S ↔ E + P
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It is regenerated in its original form at
the end of the reaction
The enzyme may be considered to take
part in the reaction
Rate of the first reaction leading to formation
of ES is proportional to the product of molar
concentrations of E and S
Rate of formation of ES  [E] [S]
Rate of formation of E and P  [ES]
Rate of the second reaction leading to
formation of E and P is proportional to molar
concentration of ES
Therefore, the rate of the overall reaction
is proportional to the enzyme concentration
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But this is true only if enough substrate
is available to combine with the enzyme
Rate of the reaction should be propor-
tional to substrate concentration also
But this is possible only if enough
enzyme is available to bind the substrate
However, the availability of enzymes in
the cells is limited
Substrate concentration
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When the substrate concentration rises,
initially the velocity of the reaction rises
proportionately
But later the rise in velocity becomes
slower until a maximum velocity (Vmax) is
reached
Plot between substrate concentration and velocity
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Vmax
Vmax
2
v
[S]Km
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At Vmax, all the enzyme molecules are saturated
with substrate, and velocity cannot increase
further if the substrate concentration is raised
The substrate concentration at which the velocity
is half of Vmax is known as the Michaelis constant
(Km) of the enzyme
[ ]
[ ]
maxV Sv
Km S
=
+
.
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The relationship between the velocity of the
reaction and the substrate concentration can
be expressed by Michaelis-Menten
equation
Hence, the equation may be rewritten as:
Vmax. [S]
v =
Km
Since both Vmax and Km are constant,
v  [S]
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When the substrate concentration is very
low, the sum of Km and [S] is nearly
equal to Km as [S] is negligible
When the substrate concentration is very
high, the sum of Km and [S] is nearly
equal to [S] as Km is relatively negligible
[S] and [S] are cancelled;
the equation may be rewritten as:
v = Vmax
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Vmax.[S]
v =
[S]
Hence, the equation may be rewritten as:
When the substrate concentration is
exactly equal to Km, the sum of Km and
[S] may be taken as 2 [S]
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Thus, when the substrate concentration
is equal to Km, the velocity is half of Vmax
The equation may be rewritten as:
=
Vmax. [S] Vmax
v =
2[S] 2
Determination of Km
Every enzyme has got a
characteristic Km
Determination of Km is important in:
Study of
enzyme
kinetics
Assay of
enzyme
activity
Evaluation of
enzyme
inhibitors
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Plotting v versus [S] is a lengthy process
The velocity has to be measured at a
number of substrate concentrations
The substrate concentration has to be
raised until Vmax is reached
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Lineweaver and Burk devised a simple
method for determination of Km
Velocity is measured at a small number
(5-6) of substrate concentrations
A graph is plotted between the reciprocal
of v and the reciprocal of [S]
The
1/v versus 1/[S]
plot is known as:
Lineweaver-
Burk plot
Double
reciprocal plot
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Vmax.[S]
v =
Km + [S]
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Michaelis-Menten equation
=
Km + [S]1
v Vmax.[S]
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or
1 Km 1 1
= +
v Vmax [S] Vmax

Michaelis-Menten equation is
inverted
or =
Km1
v Vmax.[S]
[S]
Vmax.[S]
+
This is the equation for a straight line
y (y-axis) is 1/v
a (slope of the line) is Km/Vmax
x (x-axis) is 1/[S]
b (y-intercept) is 1/Vmax
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Vmax
1 Km 1 1
v Vmax [S]
=  +
y = a x + b
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At the x-intercept (where the line meets
the x-axis), the value of y = 0
Therefore, at the x-intercept:
ax + b = 0
or ax = – b
or x = –
a
b
or
On substituting the values of b and a:
x =
1 Km
Vmax Vmax
- 
or x =
1
Vmax
-
Km
Vmax

x =
1
Km
-
Thus, the x-intercept i.e. the value of 1/[S] at
the x-intercept gives the value of 1/Km, and
the reciprocal of this will be the Km
11
1
1
Vmax
[S]Km
v
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Allosteric enzymes do not follow
Michaelis-Menten equation
The v versus [S] plot of allosteric
enzymes is sigmoidal
This shows co-operative binding of
substrate to the enzyme
[S] → [S] →
↑
v
↑
v
Substrate concentration vs velocity plot
Normal
enzyme
Allosteric
enzyme
↑
v
[S] →
Positive effectors shift the plot to the left,
and negative effectors shift it to the right
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Effect of allosteric activator and inhibitor on velocity
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Kinetics of allosteric enzymes follow the
Hill equation
Hill plot is plotted between log v/Vmax–v
and log [S]
S50 of allosteric enzymes can be
determined from the Hill plot
S50 is the substrate concentration at
which the velocity is half of Vmax
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In coenzyme-requiring reaction, coenzyme
concentration of also affects the velocity
Some coenzymes form an integral part of
the holoenzyme molecule
Other coenzymes act as co-substrates in
the reaction
Coenzyme concentration
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If the coenzyme is an integral part of the
enzyme, the effect of coenzyme
concentration is same as that of enzyme
concentration
If the coenzyme acts as a second substrate,
the effect of coenzyme concentration is
similar to that of substrate concentration
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To see the effect of temperature, velocity
of a reaction is measured at different
temperatures
A curve is plotted between velocity and
temperature
A bell-shaped curve is obtained
Temperature
↑
v
Temp →
Optimum
temp
│
Effect of temperature on velocity
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When the temperature rises, the velocity
initially increases
This is due to increase in the kinetic
energy of the reactants
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A further rise in temperature leads to
progressive denaturation of the enzyme
The velocity begins to decrease as the
enzyme gets denatured
The reaction practically stops when the
enzyme is completely denatured
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The temperature at which the velocity is
maximum is known as the optimum
temperature of the enzyme
For all human enzymes, the optimum
temperature is 37°C
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Temperature coefficient (Q10) of an
enzyme is the number of times the velocity
rises when temperature rises by 10°C
For most of the enzymes, the temperature
coefficient is two
This means that the velocity is doubled
when the temperatures rises by 10°C
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If velocity is measured at different pH levels,
and is plotted against pH, a bell-shaped
curve is obtained
A change in pH alters electrical charges on
the enzyme molecules, and often on
substrate molecules as well
This may affect binding of the substrate to
the enzyme or the catalytic activity of the
enzyme or both
pH
↑
v
pH →
Optimum
pH
│
Effect of pH on velocity
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At an optimum pH, the velocity of the
reaction is the highest because:
The electrical charges on the enzyme and
the substrate are the most suitable for:
Enzyme-substrate
binding
Catalysis
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As we move away from the optimum pH,
the velocity of the reaction decreases
At extremely low or high pH, the enzyme
may be denatured
The optimum pH is different for different
enzymes
Enzyme inhibition
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Catalytic activity of some enzymes can
be inhibited by certain compounds
Enzyme inhibition may be of two
types:
Competitive Non-competitive
Competitive inhibition
EMB-RCG
This is also known as substrate-analogue
inhibition
The inhibitor has a close structural
resemblance with the substrate
Inhibitor (I) binds to the substrate site of
enzyme forming enzyme-inhibitor (EI) complex
Substrate
Inhibitor
Products ‒‒
EMB-RCG
However, the inhibitor cannot form the
product
Thus, in the presence of the inhibitor, the
catalytic activity of the enzyme is inhibited
The inhibitor competes with the substrate
to bind to the enzyme
Substrate
+
Inhibitor
+
Enzyme
Inhibitor
+
Enzyme
Substrate
+
Enzyme
I IS
EE E
EMB-RCG
Due to competition between substrate and
inhibition, this type of inhibition is known as
competitive inhibition
Both ES and EI complexes are formed but
only ES can form the product
E + S + I ES + EI
E + P
EMB-RCG
The relative amounts of ES and EI complexes
depend upon the relative concentrations of the
substrate and the inhibitor
If the inhibitor concentration is higher, more EI
complex will be formed resulting in decreased
formation of the product
If the substrate concentration is higher, more ES
complex will be formed, and the inhibition will be
less
EMB-RCG
If a Lineweaver-Burk plot is plotted in the
presence of competitive inhibitor, the y-intercept
(1/Vmax) remains unchanged
However, the apparent Michaelis constant (K’m) is
higher (1/K’m is lower) in the presence of
competitive inhibitor
1/[S] →1
Km
1
Km´
In the absence
of inhibitor
1
Vmax
1
v
‒ In the presence
of inhibitor
↑
Competitive inhibition
‒
Competitive inhibitors do not affect the Vmax
But more substrate is required to reach the
Vmax in the presence of the inhibitor
The Vmax can be attained even in the
presence of the inhibitor
EMB-RCG
Efficacy of a competitive inhibitor can be
evaluated by measuring Km in the presence
and in the absence of the inhibitor
The inhibitors that raise the Km to a higher
degree are more effective inhibitors
Many competitive inhibitors are used as
drugs
EMB-RCG
Some competitive inhibitors
used as drugs are:
Amethopterin and aminopterin
Allopurinol
Physostigmine and neostigmine
Mevastatin and lovastatin
Amethopterin and aminopterin
Structural analogues of folic acid
Inhibitors of dihydrofolate reductase
H N2 N
N
|
OH
1
2
3
4
N
5
6
7
8
N
9 10
CH — N —2 — C — N — CH
| |
H COOH
COOH
|
CH2
|
CH2
|
O
||
H
|
Pteridine para-Amino-
benzoic acid
Glutamic
acid
Pteroylgutamic acid (folic acid)
CH3
Folic acid
Amethopterin
H N2 N
N
|
OH
1
2
3
4
N
5
6
7
8
N
9 10
CH —N —2 — C — N — CH
| |
COOH
COOH
|
CH2
|
CH2
|
O
||
H
|
CH3
Dihydrofolate
Tetrahydrofolate
Dihydrofolate
reductase
Folate
Dihydrofolate
reductase
EMB-RCG
Tetrahydrofolate is required for the synthesis
of purine and thymine nucleotides
NADPH + H+
NADPH+
NADPH + H+
NADPH+
Inhibition of dihydrofolate reductase decreases
the availability of nucleotides
If nucleotides are not available, DNA synthesis
and cell division are inhibited
Therefore, amethopterin and aminopterin are
used in cancer to suppress cell division
EMB-RCG
EMB-RCG
Allopurinol
Structural analogue of
hypoxanthine
Inhibitor of xanthine
oxidase
EMB-RCG
N
HN
O
||
C
C
CHC
N
H
H
C
N
N
HN
O
||
C
C
CHC
N
H
N
CH
Hypoxanthine Allopurinol
Hypoxanthine
Xanthine
oxidase
Uric acidXanthine
Xanthine
oxidase
Allopurinol is used to inhibit formation of
uric acid in gout, which results from over-
production of uric acid
Xanthine oxidase converts hypoxanthine
into xanthine, and xanthine into uric acid
EMB-RCG
Physostigmine and neostigmine
Structural analogues of
acetylcholine
Inhibitors of acetyl
cholinesterase
EMB-RCG
Acetylcholine + H2O
Acetate + Choline
Acetyl
cholinesterase
Physostigmine and neostigmine decrease
the breakdown of acetylcholine
They are used in the treatment of
myasthenia gravis, an auto-immune
disorder
Acetylcholine receptors are decreased in
number in myasthenia gravis
EMB-RCG
EMB-RCG
Mevastatin and Lovastatin
Structural analogues of HMG CoA
Inhibitors of HMG CoA reductase
HMG CoA Mevalonate
HMG CoA
reductase
Cholesterol
Therefore, mevastatin and lovastatin are used as
hypo-cholesterolaemic drugs
Inhibition of this reaction decreases the
synthesis of cholesterol
This is the key reaction in synthesis of cholesterol
Non-competitive inhibition
EMB-RCG
The non-competitive inhibitors have no
structural resemblance with the substrate
They do not compete with the substrate for
the substrate site on the enzyme
They bind to some other region of the
enzyme and render it inactive
Enzyme + Substrate +
Inhibitor
Enzyme + Substrate
Non-competitive inhibition
EMB-RCG
Non-competitive inhibition may be reversible
or irreversible
Generally it is irreversible
Examples are iodoacetamide, p-chloro-
mercuribenzoate, heavy metals etc
EMB-RCG
In the presence of a non-competitive
inhibitor, Lineweaver-Burk plot shows that:
This means that non-competitive inhibitors
lower the Vmax but do not affect the Km
y-intercept is higher
x-intercept is unchanged
In the presence
of inhibitor
In the absence
of inhibitor
↑
1
v
1/[S] →1
Km
1
Vmax
1
V’max
Non-competitive inhibition
Enzymes of diagnostic importance
EMB-RCG
A large number of enzymes are synthesized in
the cells
They are continuously released into circulation
due to normal wear and tear of cells
They are removed from circulation by
degradation or excretion
EMB-RCG
Non-functional plasma enzymes or
non-plasma-specific enzymes
Functional plasma enzymes or
plasma-specific enzymes
The circulating enzymes may be divided
into two types:
These enzymes are normally present in
circulation in minute concentrations
Functional plasma enzymes or plasma-
specific enzymes
EMB-RCG
These enzymes are purposely secreted
into circulation to perform specific catalytic
functions
These include lipoprotein lipase, blood
coagulation factors, complement proteins
etc
Non-functional plasma enzymes or non-
plasma-specific enzymes
EMB-RCG
These enzymes do not perform their
catalytic functions .in plasma
These are the intracellular enzymes
which enter the circulation when the cells
in which they are synthesized disintegrate
EMB-RCG
When breakdown of cells is occurring at normal
rate, non-functional enzymes are present in
plasma in very low concentrations
If the rate of destruction of cells increases due to
some pathological condition, these enzymes will
be released into circulation in large amounts
Their concentrations in plasma will rise many
times above normal
A non-functional plasma enzyme can pin-
point the site of the disease
EMB-RCG
IF
It has a selective tissue distribution
It is present in far higher concentration in
some tissues than elsewhere in the body
OR
EMB-RCG
Thus, it is the non-functional plasma
enzymes having a selective tissue
distribution which can give information
of diagnostic importance
Plasma enzymes that are established
diagnostic tools:
• Lactate dehydrogenase (LDH)
• Transaminases (GOT and GPT)
• Creatine kinase (CK)
• Gamma-glutamyl transpeptidase (GGT)
• Alkaline phosphatase (ALP)
• Acid phosphatase (ACP)
• Amylase
• Lipase
• Ceruloplasmin
EMB-RCG
Lactate
dehydrogenase
(LDH)
Catalyses
interconversion of
pyruvate and lactate
Tissue distribution
very wide
Concentration much
higher in
myocardium,
muscles and liver
EMB-RCG
Plasma LDH rises in:
Myocardial infarction
Viral hepatitis
Muscle injuries
EMB-RCG
In myocardial infarction:
Rise begins 24 hours after
infarction
Peak value is reached in
about three days
Level returns to normal in
about a week
EMB-RCG
Transaminases
Most important are glutamate oxaloacetate
transaminase (GOT) and glutamate pyruvate
transaminase (GPT)
Also known as aspartate aminotransferase
(AST) and alanine aminotransferase (ALT)
respectively
Present in high concentrations in myocardium,
liver and muscles
EMB-RCG
Serum GOT and GPT
are raised in:
Myocardial infarction
Viral hepatitis
Muscle injuries
EMB-RCG
Rise in plasma GOT is more in
myocardial infarction and that in
GPT is more in viral hepatitis
Therefore
Concentration of GOT is higher than
that of GPT in myocardium while
the situation is reverse in liver
Creatine + ATP ↔ Creatine ~ ℗ + ADP
EMB-RCG
Creatine kinase (CK)
Also known as creatine
phosphokinase (CPK)
Catalyses interconversion of
creatine and creatine phosphate
EMB-RCG
Creatine kinase is
present in:
Myocardium
Muscles
Brain
EMB-RCG
Serum CK is raised in:
Myocardial infarction
Myopathies
Muscle injuries
Rise begins within 3-6 hours after infarction
Peak is reached in 24 hours
Returns to normal in three days
More specific and early indicator than others
Serum CK in myocardial infarction
Days
Enzyme
level
Upper limit
of normal
0 1 2 3 4 5 6 7
CK GOT LDH
Begins to
rise in
Reaches
peak in
Returns to
normal in
Specificity
Myoglobin 1-3 hrs 4-6 hrs 18-24 hrs Low
Cardiac
Cardiac
troponin T
troponin I
4-6 hrs 18-36 hrs 5-15 days High
4-6 hrs 12-24 hrs 5-10 days High
Non-enzyme markers of myocardial
infarction
EMB-RCG
Is an early indicator of
alcoholic hepatitis
Serum level increases in most of
the liver diseases
Gamma-glutamyl
transpeptidase (GGT)
Transfers the g-glutamyl residue of
glutathione to other substrates
EMB-RCG
Alkaline phosphatase (ALP)
A group of enzymes that hydrolyse organic
phosphate esters at an alkaline pH
Released in circulation mainly from bones
and liver
Smaller amounts come from intestines and
placenta
Liver excretes ALP in bile
Viral hepatitis
Rickets
Hyperparathyroidism
Osteosarcoma
Bony metastases
EMB-RCG
Maximum rise in plasma ALP occurs
in obstructive jaundice
Smaller elevations occur in:
EMB-RCG
Acid phosphatase (ACP)
A group of enzymes that hydrolyse
organic phosphate esters at an acidic pH
The main source of ACP is the
prostate gland
Serum ACP is elevated in metastatic
carcinoma of prostate
EMB-RCG
Amylase
A digestive enzyme synthesised in
the pancreas and the parotid gland
Sharp elevation of serum amylase
occurs in acute pancreatitis
A smaller elevation occurs in
acute parotitis
EMB-RCG
Lipase
A lipolytic enzyme released into
circulation from the pancreas
Serum lipase rises in acute
pancreatitis
EMB-RCG
Ceruloplasmin
A copper-containing protein having
ferroxidase activity
Absent or almost absent in serum in
Wilson’s disease (hepatolenticular
degeneration)
Isoenzymes
EMB-RCG
Enzymes that:
Exist in multiple molecular forms
Catalyse the same reaction
Differ slightly in physical, chemical
and immunological properties
EMB-RCG
Isoenzymes possess quaternary
structure
They are made up of two or more
different subunits
The subunits have slightly different
primary structures
EMB-RCG
Isoenzymes Usually differ in their Km and
Vmax values
They may differ in how they are
regulated
They help in fine-tuning of metabolism
EMB-RCG
Isoenzymes can be separated by:
Electrophoresis
Chromatography
Immunochemical methods
EMB-RCG
The tissue distribution of isoenzymes
is highly specific
Measurement of isoenzymes can be
of great diagnostic importance
EMB-RCG
Isoenzymes of diagnostic
importance include:
Lactate dehydrogenase
Creatine kinase
Alkaline phosphatase
Lactate dehydrogenase
H subunit M subunit
EMB-RCG
First enzyme shown to exist in the form of
five isoenzymes by Markert (1957)
The enzyme is a tetramer made up of
two types of subunits – H and M
EMB-RCG
• HHHH
• HHHM
• HHMM
• HMMM
• MMMM
The subunits can form five different
tetramers (isoenzymes):
or LD5 or LDH5
or LD4 or LDH4
or LD3 or LDH3
or LD2 or LDH2
or LD1 or LDH1
EMB-RCG
The LD isoenzymes in plasma can be
separated by electrophoresis
The normal pattern of LD isoenzymes in
serum is LD2 >LD1 >LD3 >LD4 >LD5
EMB-RCG
The predominant isoenzymes in myocardium
are LD1 and LD2
Both are raised in myocardial infarction
The rise in LD1 is greater than that in LD2
Therefore, the pattern of plasma LD iso-
enzymes becomes LD1 >LD2 >LD3 >LD4 >LD5
EMB-RCG
LD5 is the predominant isoenzyme in liver
Therefore, LD5 is raised in viral
hepatitis
Creatine kinase
B subunit M subunit
EMB-RCG
A dimer made up of two types of
subunits
The subunits are – B and M
EMB-RCG
Three different dimers (isoenzymes) can
be formed from these two subunits:
• BB or CK1 or CK-BB
• MB or CK2 or CK-MB
• MM or CK3 or CK-MM
EMB-RCG
CK-MB is commonly measured by immuno-
inhibition
Serum is treated with anti-M subunit antibody
CK-MM is inhibited
The residual enzyme is taken to be CK-MB
as CK-BB is negligible
The major isoenzyme in myocardium is CK-MB
In plasma, CK-MB is less than 3% of total CK
CK-MB is raised in myocardial infarction
CK-BB
CK-MB
CK-MM
EMB-RCG
CK-BB, CK-MB and CK-MM are present in
cytosol
A different CK is present in mitochondria –
mitochondrial CK (CK-MT or CK-Mi)
EMB-RCG
CK-MT has two isoforms: CK-MT1 and
CK-MT2
CK-MT1 is ubiquitous
CK-MT2 is present in skeletal and heart
muscle
EMB-RCG
CK-MT can exist as a dimer or an octamer
The dimeric and octameric forms are
inter-changeable
EMB-RCG
CK-MT1 and CK-MT2 are encoded by
different genes
Thus, there are four genes for CK
subunits
These are CK-M, CK-B, CK-MT1 and CK-
MT2
EMB-RCG
CK-M and CK-B genes encode the
cytosolic enzyme
CK-MT1 and CK-MT2 genes encode the
mitochondrial enzyme
CK-MT1 and CK-MT2 isoenzymes have no
diagnostic importance
EMB-RCG
Bone, liver, intestine and placenta form
different isoenzymes
ALP isoenzymes are commonly separated
by electrophoresis
The liver isoenzyme moves the fastest
It occupies the same position as a2-globulin
Alkaline phosphatase
EMB-RCG
The bone ALP closely follows the liver
ALP
The placental isoenzyme follows the bone
isoenzyme
The intestinal isoenzyme is the slowest
moving
EMB-RCG
The liver ALP is raised in liver cancer and
biliary obstruction
The bone ALP is raised in osteoblastic
bone tumours and Paget’s disease
The placental and intestinal isoenzymes
have no diagnostic importance
EMB-RCG
Two atypical ALP isoenzymes are seen in
some cancers
These are Regan isoenzyme and Nagao
isoenzyme
These two resemble the placental
isoenzyme
EMB-RCG
Regan isoenzyme is raised in cancer of
breast, lungs, colon, uterus and ovaries
Nagao isoenzyme is raised in germ cell
cancer of the testes
EMB-RCG
Metabolic pathways need precise regulation
Regulation ensures adequacy of products with
no wastage of raw materials
Requirements of the organism keep on changing
Regulatory mechanisms must be responsive
to these changes
Regulation of enzymes
Concentrations of enzymes
Catalytic activity of enzymes
Metabolic pathways are regulated by
changing one of the following:
Enzymes play a crucial role in the
regulatory mechanisms
The regulation involves one or a few “key”
enzymes in a pathway
EMB-RCG
The rate-limiting step in the pathway
The committed step in the pathway
The key enzyme (or regulatory enzyme) may
catalyse:
EMB-RCG
Rate-limiting
step
An early reaction
that controls the
availability of
substrates for the
subsequent
reactions
Committed
step
The earliest
irreversible
reaction unique
to the pathway
Regulation of enzyme concentration
EMB-RCG
Some pathways are regulated by changing the
concentrations of the key enzymes
The rates of reactions would change accordingly
Concentration of an enzyme may be changed by
altering its synthesis or its degradation
Regulation of enzyme synthesis is commoner
Regulation of enzyme synthesis
EMB-RCG
Enzyme synthesis may be
regulated by:
Induction of enzyme synthesis
Repression of enzyme synthesis
Conversion of proenzyme into
enzyme
EMB-RCG
Enzymes may be divided into:
Constitutive
enzymes
Inducible
enzymes
Induction
EMB-RCG
Constitutive
enzymes
Inducible
enzymes
Continuously
synthesized
Synthesized only
when required
Always present in the
cell
Synthesized when
inducer enters the cell
EMB-RCG
Inducer may be the substrate for the
enzyme or may be a gratuitous inducer
A gratuitous inducer is one which is not a
substrate for the enzyme
EMB-RCG
The inducer acts on DNA, and increases
the expression of the gene that encodes
the enzyme
An example is induction of key enzymes
of gluconeogenesis by glucocorticoid
hormones
EMB-RCG
Synthesis of some enzymes is regulated by
repression
Transcription of gene encoding the enzyme
is blocked by a repressor
The repressor is made up of apo-repressor
and co-repressor
Repression
EMB-RCG
Apo-repressor is a protein always
present in the cell
When co-repressor enters or
accumulates in the cell, it combines with
apo-repressor to form the repressor
The co-repressor is generally the
product of the pathway
EMB-RCG
An example is regulation of haem synthesis
by d-aminolevulinic acid synthetase
Haem acts as co-repressor, and represses the
synthesis of this early enzyme in the pathway
When the product is used up, the repression is
relieved (derepression)
Conversion of proenzyme into enzyme
EMB-RCG
Sometimes, the concentration of enzymes needs
to be increased quickly
For example, when food enters stomach,
concentration of pepsin needs to be raised quickly
This can not be done by induction or derepression
which are slow processes
EMB-RCG
The enzyme is synthesized in the form of an
precursor, pepsinogen
Pepsinogen is an inactive proenzyme
The proenzyme will not digest the mucosal
proteins
EMB-RCG
Entry of food in the stomach generates some
signals
These signals convert pepsinogen into pepsin
The enzyme concentration is raised quickly
Proenzyme
Enzyme
Peptide
Proteolysis
Active site
(masked) →
Active site
(exposed) →
Proteolytic activation of proenzyme
Substrate
EMB-RCG
Enzyme concentration may also be
regulated by altering its breakdown
Increased breakdown will decrease the
concentration of the enzyme
Decreased breakdown will increase the
concentration of the enzyme
Regulation of enzyme degradation
EMB-RCG
Regulation of degradation is not common in
higher organisms
A few examples are seen in starvation in which
nutrients need to be conserved
Concentration of some enzymes is increased by
decreasing their breakdown
An example of such enzyme is tryptophan
pyrrolase
EMB-RCG
Regulation of catalytic activity of enzymes
Enzyme concentration remains unchanged
but its catalytic activity is altered
The catalytic activity may be altered by:
Allosteric regulation
of the enzyme
Covalent modification
of the enzyme
EMB-RCG
Allosteric regulation
This mechanism is used in some long
metabolic pathways
The substrate is converted into a product by
a series of reactions
The earliest functionally irreversible reaction is
catalysed by an allosteric enzyme
S I1 I2 I3 I4 P
E1 E2 E3 E4 E5
EMB-RCG
Usually, the product of the pathway is
the allosteric inhibitor of the enzyme
When the product accumulates, it
inhibits the allosteric enzyme
Θ
EMB-RCG
When the product is used up, the inhibition is
relieved
In this way, the rate of synthesis of product is
regulated according to the rate of its utilisation
If the pathway has a number of irreversible steps,
regulation may occur at a number of steps
EMB-RCG
Some enzymes are regulated by positive
allosteric modulation (activation)
An example is regulation of carbamoyl phosphate
synthetase I (mitochondrial)
This enzyme is allosterically activated by
N-acetylglutamate
EMB-RCG
Many enzymes are regulated by negative
allosteric modulation (inhibition)
An example is asparate transcarbamoylase
It is an early enzyme in de novo synthesis of
pyrimidine nucleotides
It is inhibited by cytidine triphosphate, a product
of the pathway
EMB-RCG
A few enzymes are subject to positive as well as
negative allosteric regulation
Phosphofructokinase-1, a regulatory enzyme in
the glycolytic pathway, is subject to:
Allosteric activation
by AMP
Allosteric inhibition
by ATP
Covalent modification
EMB-RCG
The enzymes regulated by this mechanism can
exist in two forms
These can be converted into each other by a
covalent modification of the enzyme molecule
The most common covalent modification is
addition or removal of phosphate
Phosphate is usually added to or removed from a
serine residue in the enzyme
A protein kinase adds phosphate, and a protein
phosphatase removes phosphate
P
Protein kinase
Protein phosphatase
H2O
ATP ADP
Pi
ENZYME‒Ser‒OH ENZYME‒Ser‒O‒
(Dephosphorylated
enzyme)
(Phosphorylated
enzyme)
EMB-RCG
One form, either phosphorylated or dephospho-
rylated, is active and the other is inactive
Whether the enzyme is active or inactive
depends upon the relative activities of protein
kinase and protein phosphatase
These, in turn, are controlled by hormones acting
through second messengers
EMB-RCG
An example is glycogen synthetase ‒ active in
the dephosphorylated form and inactive in the
phosphorylated form
Another example is glycogen phosphorylase ‒
inactive in the dephosphorylated form and active
in the phosphorylated form
For example, acetyl CoA carboxylase is
subject to:
Repression
Allosteric regulation
Covalent modification
Induction
Some enzymes are regulated by
multiple mechanisms
Assay of enzymes
EMB-RCG
Measurement of enzyme levels is often required
for diagnostic/academic purposes
Enzyme concentrations are very minute
Isolation and purification of individual enzymes is
laborious
Therefore, direct measurement of enzyme
concentrations is very difficult
EMB-RCG
Enzyme concentrations are measured
indirectly
Velocity of the enzyme-catalysed reaction is
measured
Conditions are such that rate of reaction is
proportional to the enzyme concentration
EMB-RCG
To keep temperature constant, reaction is carried
out in a fixed-temperature water-bath or incubator
Optimum pH is maintained by using a buffer
Substrate concentration is kept constant and high
Under such conditions, rate of the reaction will be
proportional to the enzyme concentration
EMB-RCG
The rate of the reaction can be
determined by measuring:
The rate of disappearance
of the substrate
Rate of appearance of the
product
EMB-RCG
In endpoint methods:
The reaction is carried out for a fixed
period
Initial and final concentrations of the
substrate or the product are measured
EMB-RCG
In kinetic methods, the concentration of the
substrate or the product is measured at
regular intervals for a brief period
The result in either case is expressed in
arbitrary units of enzyme activity rather
than enzyme concentration
EMB-RCG
Many enzymes are used as tools in
diagnostic and research laboratories
Glucose oxidase and peroxidase are
used for measuring glucose concentration
Hexokinase and glucose-6-phosphate
dehydrogenase are also used for
measuring glucose concentration
Enzymes as laboratory tools
EMB-RCG
Cholesterol esterase, cholesterol oxidase
and peroxidase are used for measuring
cholesterol concentration
Lipase, glycerol kinase, glycerol phosphate
oxidase and peroxidase are used for
measuring triglyceride concentration
EMB-RCG
Urease is used for measurement of urea
concentration
Uricase is used for measuring uric acid
concentration
Enzymes like peroxidase and alkaline
phosphatase are used to label antibodies
in ELISA
EMB-RCG
A number of enzymes are used in
recombinant DNA technology e.g.
Restriction endonuclease
DNA ligase
Terminal transferase
S1 nuclease
Reverse transcriptase
Taq polymerase
Enzymes as drugs
EMB-RCG
Some human, animal, plant and microbial
enzymes are used as drugs also
Digestive enzymes e.g. diastase, papain, pepsin,
chymotrypsin etc are used to aid digestion
Pancreatic amylase, lipase and proteases are
used in the treatment of pancreatic insufficiency
Serratiopeptidase is a bacterial proteolytic
enzyme
It is used to remove dead tissue from the
site of inflammation to accelerate healing
It is also used to reduce inflammation,
oedema and pain
Hyaluronidase catalyses hydrolysis of
hyaluronic acid
Hyaluronidase injections are used to
facilitate delivery of other injectable drugs
Asparaginase is used in the chemotherapy
of leukaemia
Leukaemic cells are deficient in asparagine
synthetase
They are dependent on pre-formed
asparagine
Asparaginase converts asparagine into
aspartate
This deprives the leukaemic cells of an
essential nutrient
EMB-RCG
Thrombolytic drugs used to clear
blockage of blood vessels are:
Streptokinase
Urokinase
Tissue plasminogen activator
Enzymes

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Enzymes

  • 1. R.C. Gupta Professor and Head Dept. of Biochemistry National Institute of Medical Sciences Jaipur, India Enzymes
  • 2. A vast multitude of chemical reactions occur in living organisms It is these reactions that keep the organism going These reactions would occur at extremely low velocities in the absence of catalysts EMB-RCG
  • 3. EMB-RCG Common catalysts used in non-living systems are: Acids Alkalis Metals These are not suitable for living organisms because of their: Toxicity Lack of specificity
  • 4. Biological catalysts should be: Safe (non-toxic) Specific (generally catalyzing one reaction only) Capable of adjusting their catalytic activity All these properties are present in enzymes EMB-RCG
  • 5. Enzymes were first discovered in yeast (enzyme means ‘in yeast’) EMB-RCG Chemically, all enzymes were found to be proteins They could catalyze reactions outside the living organisms also They were later found in other living organisms as well
  • 6. Definition EMB-RCG But this definition is not entirely correct Enzymes are protein catalysts that catalyse chemical reactions in biological systems Some RNA molecules (ribozymes) have been found to catalyze some reactions
  • 7. The reactant on which the enzyme acts is known as the substrate of the enzyme EMB-RCG Substrate Product Enzyme The enzyme converts the substrate into a product or products
  • 8. EMB-RCG If an enzyme catalyses a number of reactions, it will be impossible to regulate individual reactions Enzyme specificity However, the enzymes are highly specific
  • 9. EMB-RCG Generally, one enzymes catalyses only one reaction This is of crucial importance for regulation of metabolic pathways
  • 10. EMB-RCG Enzyme specificity may have the following orders: Group specificity Substrate specificity Stereo-specificity
  • 11. EMB-RCG Group specificity Enzyme is specific for a bond but not for the actual substrate Group-specific or bond-specific enzymes are commonly present in digestive secretions
  • 12. EMB-RCG For example, pepsin is specific for peptide bond but not for any protein Thus, a large variety of dietary proteins can be digested by the same enzyme Trypsin, chymotrypsin, nucleases, lipases and glycosidases are other examples
  • 13. EMB-RCG Some group-specific enzymes have a slightly higher degree of specificity For example, aminopeptidase hydrolyses only N-terminal peptide bond Carboxypeptidase hydrolyses only the C-terminal peptide bond Endopeptidases hydrolyse the internal peptide bonds only
  • 15. EMB-RCG Most enzymes are specific for a chemical bond/group as well as the substrate For example, glucokinase and fructokinase are substrate-specific enzymes They transfer a phosphate group from ATP to one specific substrate Substrate specificity
  • 16. Glucose Glucose-6-Phosphate Glucokinase ATP ADP Fructose Fructose-1-Phosphate Fructokinase ATP ADP EMB-RCG
  • 17. EMB-RCG Stereo-specificity Many biomolecules exhibit stereo- isomerism Examples are carbohydrates and amino acids Enzymes acting on these are specific for one stereo-isomer
  • 18. EMB-RCG Mammalian enzymes acting on carbo- hydrates are generally specific for D-isomers Those acting on amino acids are generally specific for L-isomers Exceptions are racemases which inter-convert the D- and L-isomers
  • 19. EMB-RCG COOH I H2N – C – H I CH3 COOH I H – C – NH2 I CH3 Alanine racemase L-Alanine D-Alanine Stereospecificity – An exception
  • 20. Some enzymes require a non-protein substance for their catalytic activity If the non-protein substance is organic, it is known as a coenzyme If the non-protein substance is inorganic, it is known as a cofactor EMB-RCG Coenzymes and cofactors
  • 21. EMB-RCG The coenzyme or the cofactor may be: An integral part of the enzyme or Its presence may be required during the reaction
  • 22. The protein portion of an enzyme that requires a coenzyme is called apoenzyme Apoenzyme + Coenzyme → Holoenzyme EMB-RCG Apoenzyme combines with coenzyme to form the active holoenzyme
  • 24. EMB-RCG The coenzymes generally contain vitamins of B-complex family Some are converted into coenzymes e.g. thiamin, riboflavin, niacin, pantothenic acid, pyridoxine, folic acid and vitamin B12 Some act as coenzymes by themselves e.g. biotin
  • 26. EMB-RCG Coenzymes can be divided into two groups: Coenzymes involved in transfer of hydrogen Coenzymes involved in transfer of groups other than hydrogen
  • 27. Coenzymes involved in transfer of hydrogen: Flavin mononucleotide (FMN) Flavin adenine dinucleotide (FAD) Nicotinamide adenine dinucleotide (NAD+) Nicotinamide adenine dinucleotide phosphate (NADP+) Lipoic acid Coenzyme Q
  • 28. Coenzymes involved in transfer of groups other than hydrogen: Thiamin pyrophosphate (TPP) Coenzyme A (Co A) Pyridoxal phosphate (PLP) Tetrahydrofolate (H4- Folate) Cobamides (B12- Coenzymes) Lipoic acid Biotin ATP & similar nucleotides
  • 29. EMB-RCG Role of coenzymes The enzyme acts upon its substrate, and converts it into a product Coenzyme acts as a co-substrate or a second substrate in the group transfer reactions The coenzyme either donates or accepts the group that is being transferred
  • 30. EMB-RCG In the second reaction, the coenzyme NAD+ acts a second substrate and accepts the hydrogen atoms In the first reaction, the coenzyme ATP acts as a second substrate and donates a phosphate group CH2‒OH CH2‒OH CH‒OH Glycerol CH2‒OH CH2‒O‒ CH‒OH CH2‒OH CH2‒O‒ C = O ATP Glycerol kinase ADP Glycerol-3- phosphate Dihydroxy- acetone phosphate Glycerol-3- phosphate dehydrogenase NAD+ NADH + H+
  • 31. The chemical change in the coenzyme is opposite to that in the substrate EMB-RCG Thus, they act only as carriers, and regain their original form at the end of the reaction Pyridoxal phosphate, for example, acts as a carrier of amino group in transamination Some coenzymes accept a chemical group from one substrate and donate it to another
  • 32. EMB-RCG Aspartate Glutamate Oxaloacetate a-Ketoglutarate Pyridoxal phosphate Pyridoxamine phosphate Glutamate oxaloacetate transaminase (GOT)
  • 33. Pyridoxal phosphate first accepts the amino group from aspartate, and is converted into pyridoxamine phosphate Pyridoxamine phosphate then transfers the amino group to a-ketoglutarate, and is converted into pyridoxal phosphate In the coupled reaction, aspartate is converted into oxaloacetate, and a-ketoglutarate is converted into glutamate EMB-RCG
  • 34. EMB-RCG Aspartate + a-Ketoglutarate Oxaloacetate + Glutamate GOT PLP Though pyridoxal phosphate is a reactant, the reaction is usually shown as: The coenzyme goes back to its original form at the end of the reaction
  • 35. EMB-RCG Sometimes, the change in the coenzyme is more important than that in the substrate In glycolysis, glucose is converted into pyruvate, and NAD+ is reduced in one reaction Reduced NAD+ transfers its hydrogen atoms to oxygen, and NAD+ is regenerated
  • 36. EMB-RCG Here, regeneration of NAD+ is more important for continuation of glycolysis One more reaction occurs in which pyruvate is reduced to lactate, and NADH is oxidised to NAD+ If the conditions are anaerobic, NAD+ cannot be regenerated due to lack of oxygen
  • 38. Enzyme nomenclature and classification EMB-RCG The nomenclature of enzymes has undergone many changes over the years The names assigned to enzymes in the beginning were very vague and uninformative Some of the early names are pepsin, ptylin, zymase etc These indicate neither the substrates nor the type of reaction catalyzed by the enzyme
  • 39. EMB-RCG Later on, a slightly more informative nomen- clature was adopted Suffix -ase was added to the name of the substrate e.g. lipase, protease etc Still the type of reaction catalyzed by the enzyme remained unclear
  • 40. EMB-RCG Nomenclature was modified further, to include the name of the substrate followed by the type of reaction ending with -ase This resulted in names like lactate dehydro- genase, pyruvate carboxylase, glutamate decarboxylase etc Even these names do not give complete information, for example whether a coenzyme is required or a byproduct is formed
  • 41. EMB-RCG To make the names of enzymes informative and unambiguous, International Union of Biochemistry (IUB) formed an Enzyme Commission The enzyme commission proposed a method of nomenclature and classification of enzymes which is applicable to all living organisms
  • 42. According to IUB system: • The enzymes have been divided into six classes (numbered 1 - 6) • Each class is divided into subclasses • Subclasses are divided into subsubclasses • Subsubclasses are divided into individual enzymes
  • 43. EMB-RCG Nomenclature The name of the enzyme has two parts The first part includes the name(s) of the substrate(s) including substrate (coenzyme) The second part includes the type of reaction ending with -ase If any additional information is to be given, it is put in parenthesis at the end
  • 44. For example, the enzyme having the trivial name glutamate dehydrogenase catalyzes the following reaction: L-Glutamate + NAD(P)+ + H2 O → a-Ketoglutarate + NAD(P)H + H+ + NH3 According to IUB system, this enzyme is known as L-Glutamate: NAD(P) oxido- reductase (deaminating) EMB-RCG
  • 45. EMB-RCG The amino group of L-glutamate is released as ammonia NAD+ or NADP+ is required as a co-substrate This enzyme acts on L-glutamate The IUB name shows that: Type of reaction is oxidoreduction i.e. L-glutamate is oxidised and the co-substrate is reduced
  • 46. EMB-RCG Moreover, each enzyme has been given a code number consisting of four digits: First digit shows the number of the class Second digit shows the number of the subclass Third digit shows the number of the subsubclass Fourth digit shows the number of the enzyme
  • 47. EMB-RCG The code number of L-glutamate: NAD(P) oxidoreductase (deaminating) is EC 1.4.1.3 This shows that is it the third enzyme of subsubclass 1 of subclass 4 of class 1 EC is the acronym for Enzyme Commission
  • 48. EMB-RCG The enzymes are divided into six classes in IUB classification: Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases
  • 49. EMB-RCG Oxidoreductases These are the enzymes that catalyze oxidation-reduction reactions One of the substrates is oxidised and the other is reduced Different subclasses act on different chemical groups Groups undergoing the reaction include –CH=CH–, >CH–OH, >C=O, >CH–NH2 etc
  • 50. EMB-RCG Examples of oxidoreductases are: Glutamate dehydrogenase Lactate dehydrogenase Malate dehydrogenase Glycerol-3-phosphate dehydrogenase
  • 51. EMB-RCG Transferases These enzymes transfer a group other than hydrogen from one substrate to another Such groups include methyl group, amino group, phosphate group, acyl group, glycosyl group etc
  • 52. EMB-RCG Examples of transferases are: Hexokinase Glucokinase Glutamate oxaloacetate transaminase Ornithine carbamoyl transferase
  • 53. EMB-RCG Hydrolases These enzymes hydrolyse various bonds such as peptide, ester, glycosidic bonds etc They are commonly found in the digestive secretions and lysosomes They hydrolyse carbohydrates, lipids, proteins etc
  • 55. EMB-RCG Lyases These enzymes remove chemical groups from substrates by mechanisms other than hydrolysis The groups removed may be water, amino group, carboxyl group etc
  • 57. Isomerases These enzymes catalyse inter- conversion of isomers of compound Substrates include aldose-ketose isomers, stereo-isomers etc EMB-RCG
  • 58. Examples of isomerases are: Alanine racemase Triose phosphate isomerase Phosphohexose isomerase Ribose-5-phosphate ketoisomerase EMB-RCG
  • 59. Ligases These enzymes ligate or bind two substrates together Binding occurs by a covalent bond A source of energy is required e.g. a high-energy phosphate EMB-RCG
  • 60. Examples of ligases are: Glutamine synthetase Squalene synthetase Acetyl CoA carboxylase EMB-RCG
  • 61. At temperatures above absolute zero (– 273°C), molecules are in constant motion because of their kinetic energy EMB-RCG A chemical reaction occurs when molecules of reactants collide with each other in the correct orientation (kinetic theory of reaction) Mechanism of action of enzymes
  • 62. The greater the frequency of collisions between the reactant molecules, the greater will be the rate of reaction EMB-RCG The frequency of collisions can be increased by raising the temperature
  • 63. EMB-RCG Rise in temperature would increase: Molecular motion Frequency of collisions Rate of reaction
  • 64. Energy input required to reach the critical level is known as the energy of activation Energy level of reactants has to be raised to a critical level for the reaction to occur
  • 65. In living organisms, the enzymes provide an alternate pathway for the reaction Enzymes lower the energy of activation The option of raising temperature is not available in living organisms
  • 66.
  • 67.
  • 68.
  • 69.
  • 70. The enzyme molecules are much larger than their substrates EMB-RCG Enzyme-substrate interaction The substrate binds to this site forming an enzyme-substrate (ES) complex An enzyme possesses a specific binding site for its substrate(s) known as the substrate site
  • 71.
  • 72. Substrates bind to enzyme Bond is formed Product is released The binding may bring two substrates in close proximity (bond-forming distance) in the correct orientation so that a bond is formed between the two
  • 73. The binding of a substrate to the enzyme many induce a strain in the substrate As a result, a bond is broken in the substrate The substrate is split into two or more products which are released
  • 74. Enzyme ‒ Substrate ‒ Products ‒ Substrate binds to enzyme A strain occurs in the substrate; a bond is broken Substrate splits into products which are released
  • 75. On binding of two substrates to the enzyme, a chemical group may be transferred from one substrate to another
  • 76. The catalytic action of the enzyme may be exerted by: Cofactors Coenzymes Some amino acid residues in the substrate site EMB-RCG
  • 77. In the reaction catalysed by carbonic anhydrase, the cofactor (zinc) catalyses the reaction ‒ Zn++ H+ + HCO3 ‒ H2O ‒ Zn++ ...‒O + H+ H I CO2 ‒ Zn++ + O‒C‒O‒ + H+ H I II O ‒ Zn++ ...O‒C‒O H I II O H I ‒ Zn++ ...O + C = O...H+ H I II O ‒
  • 78. In transamination reactions, the coenzyme (pyridoxal phosphate) is involved in catalysis Pyridoxal phosphate is present at the substrate site It accepts an amino group from an amino acid, and then donates it to a keto acid EMB-RCG
  • 79.
  • 81. Common amino acid residues in the substrate site are serine, histidine, cysteine, aspartate etc Serine proteases are proteolytic enzymes in which serine residues catalyse hydrolysis Examples of serine proteases are trypsin, chymotrypsin, thrombin etc EMB-RCG
  • 82.
  • 83. The first model was proposed by Emil Fischer Also known as rigid template model A different model was later proposed by Koshland Also known as induced fit model Models of enzyme conformation EMB-RCG
  • 84. EMB-RCG Fischer’s model Conformation of enzymes very rigid Lock and key type of complementarity between substrate and enzyme Complementarity responsible for specificity of enzymes Lock Key
  • 86. Fischer’s model did not agree with certain experimental findings obtained later Conformation of enzyme was found to change when it combined with its substrate EMB-RCG
  • 87. Before substrate binding After substrate binding Substrate Enzyme
  • 88. Koshland’s model conforms to known findings In the absence of substrate, complementarity between enzyme and substrate is not apparent Approach of substrate induces change in conformation of the enzyme The substrate site becomes complementary to the substrate
  • 89. The substrate binds to the enzyme, and is converted into the product Release of the product restores the enzyme to its original conformation Change in conformation of the enzyme produces ‘induced fit’
  • 91. Allosteric enzymes Some enzymes possess a site, in addition to the substrate site, known as the allosteric site Binding of an allosteric molecule to allosteric site changes the conformation of the enzyme Enzymes having allosteric site are termed as allosteric enzymes EMB-RCG
  • 92. EMB-RCG Allosteric regulator Allosteric modifier Allosteric effector The allosteric molecule is also known as:
  • 93. Some allosteric molecules: Facilitate the conformational change required for substrate binding They are known as allosteric activators (positive modifiers) An example is N-acetylglutamate which activates carbamoyl phosphate synthetase EMB-RCG
  • 94. Enzyme Substrate site Allosteric site Substrate Allosteric activator Allosteric activator binds to enzyme; substrate site changes Substrate can now bind to substrate site
  • 95. Some allosteric regulators: Prevent the conformational change required for the binding of the substrate Such regulators are known as allosteric inhibitors (negative modifiers) An example is glucose-6-phosphate which inhibits hexokinase EMB-RCG
  • 96.
  • 97. Enzymes subject to allosteric inhibition are usually present at the start of long pathways The allosteric enzyme regulates the rate of formation of the product The allosteric inhibitor is generally the product of the pathway
  • 98. If the product is not being utilised, it will accumulate It inhibits the allosteric enzyme, and further synthesis of the product ceases When the product is used up, the allosteric enzyme becomes free and active again EMB-RCG
  • 99. E1 is an allosteric enzyme, and P is its allosteric inhibitor EMB-RCG S I1 I2 I3 I4 P E1 E2 E3 E4 E5 Θ
  • 100. Factors affecting the rates of enzyme-catalysed reactions Enzyme concentration Substrate concentration Coenzyme concentration Temperature pH EMB-RCG
  • 101. Enzyme concentration EMB-RCG An enzyme catalyses a reaction by forming enzyme-substrate complex Enzyme-substrate complex dissociates into the enzyme and the product
  • 102. E + S ↔ E S ↔ E + P EMB-RCG It is regenerated in its original form at the end of the reaction The enzyme may be considered to take part in the reaction
  • 103. Rate of the first reaction leading to formation of ES is proportional to the product of molar concentrations of E and S Rate of formation of ES  [E] [S] Rate of formation of E and P  [ES] Rate of the second reaction leading to formation of E and P is proportional to molar concentration of ES
  • 104. Therefore, the rate of the overall reaction is proportional to the enzyme concentration EMB-RCG But this is true only if enough substrate is available to combine with the enzyme
  • 105. Rate of the reaction should be propor- tional to substrate concentration also But this is possible only if enough enzyme is available to bind the substrate However, the availability of enzymes in the cells is limited Substrate concentration EMB-RCG
  • 106. EMB-RCG When the substrate concentration rises, initially the velocity of the reaction rises proportionately But later the rise in velocity becomes slower until a maximum velocity (Vmax) is reached
  • 107. Plot between substrate concentration and velocity EMB-RCG Vmax Vmax 2 v [S]Km
  • 108. EMB-RCG At Vmax, all the enzyme molecules are saturated with substrate, and velocity cannot increase further if the substrate concentration is raised The substrate concentration at which the velocity is half of Vmax is known as the Michaelis constant (Km) of the enzyme
  • 109. [ ] [ ] maxV Sv Km S = + . EMB-RCG The relationship between the velocity of the reaction and the substrate concentration can be expressed by Michaelis-Menten equation
  • 110. Hence, the equation may be rewritten as: Vmax. [S] v = Km Since both Vmax and Km are constant, v  [S] EMB-RCG When the substrate concentration is very low, the sum of Km and [S] is nearly equal to Km as [S] is negligible
  • 111. When the substrate concentration is very high, the sum of Km and [S] is nearly equal to [S] as Km is relatively negligible [S] and [S] are cancelled; the equation may be rewritten as: v = Vmax EMB-RCG Vmax.[S] v = [S] Hence, the equation may be rewritten as:
  • 112. When the substrate concentration is exactly equal to Km, the sum of Km and [S] may be taken as 2 [S] EMB-RCG Thus, when the substrate concentration is equal to Km, the velocity is half of Vmax The equation may be rewritten as: = Vmax. [S] Vmax v = 2[S] 2
  • 113. Determination of Km Every enzyme has got a characteristic Km Determination of Km is important in: Study of enzyme kinetics Assay of enzyme activity Evaluation of enzyme inhibitors EMB-RCG
  • 114. EMB-RCG Plotting v versus [S] is a lengthy process The velocity has to be measured at a number of substrate concentrations The substrate concentration has to be raised until Vmax is reached
  • 115. EMB-RCG Lineweaver and Burk devised a simple method for determination of Km Velocity is measured at a small number (5-6) of substrate concentrations A graph is plotted between the reciprocal of v and the reciprocal of [S]
  • 116. The 1/v versus 1/[S] plot is known as: Lineweaver- Burk plot Double reciprocal plot EMB-RCG
  • 117. Vmax.[S] v = Km + [S] EMB-RCG Michaelis-Menten equation
  • 118. = Km + [S]1 v Vmax.[S] EMB-RCG or 1 Km 1 1 = + v Vmax [S] Vmax  Michaelis-Menten equation is inverted or = Km1 v Vmax.[S] [S] Vmax.[S] +
  • 119. This is the equation for a straight line y (y-axis) is 1/v a (slope of the line) is Km/Vmax x (x-axis) is 1/[S] b (y-intercept) is 1/Vmax EMB-RCG Vmax 1 Km 1 1 v Vmax [S] =  + y = a x + b
  • 120. EMB-RCG At the x-intercept (where the line meets the x-axis), the value of y = 0 Therefore, at the x-intercept: ax + b = 0 or ax = – b or x = – a b
  • 121. or On substituting the values of b and a: x = 1 Km Vmax Vmax -  or x = 1 Vmax - Km Vmax  x = 1 Km -
  • 122. Thus, the x-intercept i.e. the value of 1/[S] at the x-intercept gives the value of 1/Km, and the reciprocal of this will be the Km 11 1 1 Vmax [S]Km v EMB-RCG
  • 123. EMB-RCG Allosteric enzymes do not follow Michaelis-Menten equation The v versus [S] plot of allosteric enzymes is sigmoidal This shows co-operative binding of substrate to the enzyme
  • 124. [S] → [S] → ↑ v ↑ v Substrate concentration vs velocity plot Normal enzyme Allosteric enzyme
  • 125. ↑ v [S] → Positive effectors shift the plot to the left, and negative effectors shift it to the right EMB-RCG Effect of allosteric activator and inhibitor on velocity
  • 126. EMB-RCG Kinetics of allosteric enzymes follow the Hill equation Hill plot is plotted between log v/Vmax–v and log [S] S50 of allosteric enzymes can be determined from the Hill plot S50 is the substrate concentration at which the velocity is half of Vmax
  • 127. EMB-RCG In coenzyme-requiring reaction, coenzyme concentration of also affects the velocity Some coenzymes form an integral part of the holoenzyme molecule Other coenzymes act as co-substrates in the reaction Coenzyme concentration
  • 128. EMB-RCG If the coenzyme is an integral part of the enzyme, the effect of coenzyme concentration is same as that of enzyme concentration If the coenzyme acts as a second substrate, the effect of coenzyme concentration is similar to that of substrate concentration
  • 129. EMB-RCG To see the effect of temperature, velocity of a reaction is measured at different temperatures A curve is plotted between velocity and temperature A bell-shaped curve is obtained Temperature
  • 130. ↑ v Temp → Optimum temp │ Effect of temperature on velocity
  • 131. EMB-RCG When the temperature rises, the velocity initially increases This is due to increase in the kinetic energy of the reactants
  • 132. EMB-RCG A further rise in temperature leads to progressive denaturation of the enzyme The velocity begins to decrease as the enzyme gets denatured The reaction practically stops when the enzyme is completely denatured
  • 133. EMB-RCG The temperature at which the velocity is maximum is known as the optimum temperature of the enzyme For all human enzymes, the optimum temperature is 37°C
  • 134. EMB-RCG Temperature coefficient (Q10) of an enzyme is the number of times the velocity rises when temperature rises by 10°C For most of the enzymes, the temperature coefficient is two This means that the velocity is doubled when the temperatures rises by 10°C
  • 135. EMB-RCG If velocity is measured at different pH levels, and is plotted against pH, a bell-shaped curve is obtained A change in pH alters electrical charges on the enzyme molecules, and often on substrate molecules as well This may affect binding of the substrate to the enzyme or the catalytic activity of the enzyme or both pH
  • 137. EMB-RCG At an optimum pH, the velocity of the reaction is the highest because: The electrical charges on the enzyme and the substrate are the most suitable for: Enzyme-substrate binding Catalysis
  • 138. EMB-RCG As we move away from the optimum pH, the velocity of the reaction decreases At extremely low or high pH, the enzyme may be denatured The optimum pH is different for different enzymes
  • 139. Enzyme inhibition EMB-RCG Catalytic activity of some enzymes can be inhibited by certain compounds Enzyme inhibition may be of two types: Competitive Non-competitive
  • 140. Competitive inhibition EMB-RCG This is also known as substrate-analogue inhibition The inhibitor has a close structural resemblance with the substrate Inhibitor (I) binds to the substrate site of enzyme forming enzyme-inhibitor (EI) complex
  • 142. EMB-RCG However, the inhibitor cannot form the product Thus, in the presence of the inhibitor, the catalytic activity of the enzyme is inhibited The inhibitor competes with the substrate to bind to the enzyme
  • 144. EMB-RCG Due to competition between substrate and inhibition, this type of inhibition is known as competitive inhibition Both ES and EI complexes are formed but only ES can form the product E + S + I ES + EI E + P
  • 145. EMB-RCG The relative amounts of ES and EI complexes depend upon the relative concentrations of the substrate and the inhibitor If the inhibitor concentration is higher, more EI complex will be formed resulting in decreased formation of the product If the substrate concentration is higher, more ES complex will be formed, and the inhibition will be less
  • 146. EMB-RCG If a Lineweaver-Burk plot is plotted in the presence of competitive inhibitor, the y-intercept (1/Vmax) remains unchanged However, the apparent Michaelis constant (K’m) is higher (1/K’m is lower) in the presence of competitive inhibitor
  • 147. 1/[S] →1 Km 1 Km´ In the absence of inhibitor 1 Vmax 1 v ‒ In the presence of inhibitor ↑ Competitive inhibition ‒
  • 148. Competitive inhibitors do not affect the Vmax But more substrate is required to reach the Vmax in the presence of the inhibitor The Vmax can be attained even in the presence of the inhibitor
  • 149. EMB-RCG Efficacy of a competitive inhibitor can be evaluated by measuring Km in the presence and in the absence of the inhibitor The inhibitors that raise the Km to a higher degree are more effective inhibitors Many competitive inhibitors are used as drugs
  • 150. EMB-RCG Some competitive inhibitors used as drugs are: Amethopterin and aminopterin Allopurinol Physostigmine and neostigmine Mevastatin and lovastatin
  • 151. Amethopterin and aminopterin Structural analogues of folic acid Inhibitors of dihydrofolate reductase
  • 152. H N2 N N | OH 1 2 3 4 N 5 6 7 8 N 9 10 CH — N —2 — C — N — CH | | H COOH COOH | CH2 | CH2 | O || H | Pteridine para-Amino- benzoic acid Glutamic acid Pteroylgutamic acid (folic acid) CH3 Folic acid Amethopterin H N2 N N | OH 1 2 3 4 N 5 6 7 8 N 9 10 CH —N —2 — C — N — CH | | COOH COOH | CH2 | CH2 | O || H | CH3
  • 153. Dihydrofolate Tetrahydrofolate Dihydrofolate reductase Folate Dihydrofolate reductase EMB-RCG Tetrahydrofolate is required for the synthesis of purine and thymine nucleotides NADPH + H+ NADPH+ NADPH + H+ NADPH+
  • 154. Inhibition of dihydrofolate reductase decreases the availability of nucleotides If nucleotides are not available, DNA synthesis and cell division are inhibited Therefore, amethopterin and aminopterin are used in cancer to suppress cell division EMB-RCG
  • 157. Hypoxanthine Xanthine oxidase Uric acidXanthine Xanthine oxidase Allopurinol is used to inhibit formation of uric acid in gout, which results from over- production of uric acid Xanthine oxidase converts hypoxanthine into xanthine, and xanthine into uric acid
  • 158. EMB-RCG Physostigmine and neostigmine Structural analogues of acetylcholine Inhibitors of acetyl cholinesterase
  • 159. EMB-RCG Acetylcholine + H2O Acetate + Choline Acetyl cholinesterase
  • 160. Physostigmine and neostigmine decrease the breakdown of acetylcholine They are used in the treatment of myasthenia gravis, an auto-immune disorder Acetylcholine receptors are decreased in number in myasthenia gravis EMB-RCG
  • 161. EMB-RCG Mevastatin and Lovastatin Structural analogues of HMG CoA Inhibitors of HMG CoA reductase
  • 162. HMG CoA Mevalonate HMG CoA reductase Cholesterol Therefore, mevastatin and lovastatin are used as hypo-cholesterolaemic drugs Inhibition of this reaction decreases the synthesis of cholesterol This is the key reaction in synthesis of cholesterol
  • 163. Non-competitive inhibition EMB-RCG The non-competitive inhibitors have no structural resemblance with the substrate They do not compete with the substrate for the substrate site on the enzyme They bind to some other region of the enzyme and render it inactive
  • 164. Enzyme + Substrate + Inhibitor Enzyme + Substrate Non-competitive inhibition
  • 165. EMB-RCG Non-competitive inhibition may be reversible or irreversible Generally it is irreversible Examples are iodoacetamide, p-chloro- mercuribenzoate, heavy metals etc
  • 166. EMB-RCG In the presence of a non-competitive inhibitor, Lineweaver-Burk plot shows that: This means that non-competitive inhibitors lower the Vmax but do not affect the Km y-intercept is higher x-intercept is unchanged
  • 167. In the presence of inhibitor In the absence of inhibitor ↑ 1 v 1/[S] →1 Km 1 Vmax 1 V’max Non-competitive inhibition
  • 168. Enzymes of diagnostic importance EMB-RCG A large number of enzymes are synthesized in the cells They are continuously released into circulation due to normal wear and tear of cells They are removed from circulation by degradation or excretion
  • 169. EMB-RCG Non-functional plasma enzymes or non-plasma-specific enzymes Functional plasma enzymes or plasma-specific enzymes The circulating enzymes may be divided into two types: These enzymes are normally present in circulation in minute concentrations
  • 170. Functional plasma enzymes or plasma- specific enzymes EMB-RCG These enzymes are purposely secreted into circulation to perform specific catalytic functions These include lipoprotein lipase, blood coagulation factors, complement proteins etc
  • 171. Non-functional plasma enzymes or non- plasma-specific enzymes EMB-RCG These enzymes do not perform their catalytic functions .in plasma These are the intracellular enzymes which enter the circulation when the cells in which they are synthesized disintegrate
  • 172. EMB-RCG When breakdown of cells is occurring at normal rate, non-functional enzymes are present in plasma in very low concentrations If the rate of destruction of cells increases due to some pathological condition, these enzymes will be released into circulation in large amounts Their concentrations in plasma will rise many times above normal
  • 173. A non-functional plasma enzyme can pin- point the site of the disease EMB-RCG IF It has a selective tissue distribution It is present in far higher concentration in some tissues than elsewhere in the body OR
  • 174. EMB-RCG Thus, it is the non-functional plasma enzymes having a selective tissue distribution which can give information of diagnostic importance
  • 175. Plasma enzymes that are established diagnostic tools: • Lactate dehydrogenase (LDH) • Transaminases (GOT and GPT) • Creatine kinase (CK) • Gamma-glutamyl transpeptidase (GGT) • Alkaline phosphatase (ALP) • Acid phosphatase (ACP) • Amylase • Lipase • Ceruloplasmin
  • 176. EMB-RCG Lactate dehydrogenase (LDH) Catalyses interconversion of pyruvate and lactate Tissue distribution very wide Concentration much higher in myocardium, muscles and liver
  • 177. EMB-RCG Plasma LDH rises in: Myocardial infarction Viral hepatitis Muscle injuries
  • 178. EMB-RCG In myocardial infarction: Rise begins 24 hours after infarction Peak value is reached in about three days Level returns to normal in about a week
  • 179. EMB-RCG Transaminases Most important are glutamate oxaloacetate transaminase (GOT) and glutamate pyruvate transaminase (GPT) Also known as aspartate aminotransferase (AST) and alanine aminotransferase (ALT) respectively Present in high concentrations in myocardium, liver and muscles
  • 180. EMB-RCG Serum GOT and GPT are raised in: Myocardial infarction Viral hepatitis Muscle injuries
  • 181. EMB-RCG Rise in plasma GOT is more in myocardial infarction and that in GPT is more in viral hepatitis Therefore Concentration of GOT is higher than that of GPT in myocardium while the situation is reverse in liver
  • 182. Creatine + ATP ↔ Creatine ~ ℗ + ADP EMB-RCG Creatine kinase (CK) Also known as creatine phosphokinase (CPK) Catalyses interconversion of creatine and creatine phosphate
  • 183. EMB-RCG Creatine kinase is present in: Myocardium Muscles Brain
  • 184. EMB-RCG Serum CK is raised in: Myocardial infarction Myopathies Muscle injuries
  • 185. Rise begins within 3-6 hours after infarction Peak is reached in 24 hours Returns to normal in three days More specific and early indicator than others Serum CK in myocardial infarction
  • 186. Days Enzyme level Upper limit of normal 0 1 2 3 4 5 6 7 CK GOT LDH
  • 187. Begins to rise in Reaches peak in Returns to normal in Specificity Myoglobin 1-3 hrs 4-6 hrs 18-24 hrs Low Cardiac Cardiac troponin T troponin I 4-6 hrs 18-36 hrs 5-15 days High 4-6 hrs 12-24 hrs 5-10 days High Non-enzyme markers of myocardial infarction
  • 188. EMB-RCG Is an early indicator of alcoholic hepatitis Serum level increases in most of the liver diseases Gamma-glutamyl transpeptidase (GGT) Transfers the g-glutamyl residue of glutathione to other substrates
  • 189. EMB-RCG Alkaline phosphatase (ALP) A group of enzymes that hydrolyse organic phosphate esters at an alkaline pH Released in circulation mainly from bones and liver Smaller amounts come from intestines and placenta Liver excretes ALP in bile
  • 190. Viral hepatitis Rickets Hyperparathyroidism Osteosarcoma Bony metastases EMB-RCG Maximum rise in plasma ALP occurs in obstructive jaundice Smaller elevations occur in:
  • 191. EMB-RCG Acid phosphatase (ACP) A group of enzymes that hydrolyse organic phosphate esters at an acidic pH The main source of ACP is the prostate gland Serum ACP is elevated in metastatic carcinoma of prostate
  • 192. EMB-RCG Amylase A digestive enzyme synthesised in the pancreas and the parotid gland Sharp elevation of serum amylase occurs in acute pancreatitis A smaller elevation occurs in acute parotitis
  • 193. EMB-RCG Lipase A lipolytic enzyme released into circulation from the pancreas Serum lipase rises in acute pancreatitis
  • 194. EMB-RCG Ceruloplasmin A copper-containing protein having ferroxidase activity Absent or almost absent in serum in Wilson’s disease (hepatolenticular degeneration)
  • 195. Isoenzymes EMB-RCG Enzymes that: Exist in multiple molecular forms Catalyse the same reaction Differ slightly in physical, chemical and immunological properties
  • 196. EMB-RCG Isoenzymes possess quaternary structure They are made up of two or more different subunits The subunits have slightly different primary structures
  • 197. EMB-RCG Isoenzymes Usually differ in their Km and Vmax values They may differ in how they are regulated They help in fine-tuning of metabolism
  • 198. EMB-RCG Isoenzymes can be separated by: Electrophoresis Chromatography Immunochemical methods
  • 199. EMB-RCG The tissue distribution of isoenzymes is highly specific Measurement of isoenzymes can be of great diagnostic importance
  • 200. EMB-RCG Isoenzymes of diagnostic importance include: Lactate dehydrogenase Creatine kinase Alkaline phosphatase
  • 201. Lactate dehydrogenase H subunit M subunit EMB-RCG First enzyme shown to exist in the form of five isoenzymes by Markert (1957) The enzyme is a tetramer made up of two types of subunits – H and M
  • 202. EMB-RCG • HHHH • HHHM • HHMM • HMMM • MMMM The subunits can form five different tetramers (isoenzymes): or LD5 or LDH5 or LD4 or LDH4 or LD3 or LDH3 or LD2 or LDH2 or LD1 or LDH1
  • 203. EMB-RCG The LD isoenzymes in plasma can be separated by electrophoresis The normal pattern of LD isoenzymes in serum is LD2 >LD1 >LD3 >LD4 >LD5
  • 204. EMB-RCG The predominant isoenzymes in myocardium are LD1 and LD2 Both are raised in myocardial infarction The rise in LD1 is greater than that in LD2 Therefore, the pattern of plasma LD iso- enzymes becomes LD1 >LD2 >LD3 >LD4 >LD5
  • 205. EMB-RCG LD5 is the predominant isoenzyme in liver Therefore, LD5 is raised in viral hepatitis
  • 206. Creatine kinase B subunit M subunit EMB-RCG A dimer made up of two types of subunits The subunits are – B and M
  • 207. EMB-RCG Three different dimers (isoenzymes) can be formed from these two subunits: • BB or CK1 or CK-BB • MB or CK2 or CK-MB • MM or CK3 or CK-MM
  • 208. EMB-RCG CK-MB is commonly measured by immuno- inhibition Serum is treated with anti-M subunit antibody CK-MM is inhibited The residual enzyme is taken to be CK-MB as CK-BB is negligible
  • 209. The major isoenzyme in myocardium is CK-MB In plasma, CK-MB is less than 3% of total CK CK-MB is raised in myocardial infarction CK-BB CK-MB CK-MM
  • 210. EMB-RCG CK-BB, CK-MB and CK-MM are present in cytosol A different CK is present in mitochondria – mitochondrial CK (CK-MT or CK-Mi)
  • 211. EMB-RCG CK-MT has two isoforms: CK-MT1 and CK-MT2 CK-MT1 is ubiquitous CK-MT2 is present in skeletal and heart muscle
  • 212. EMB-RCG CK-MT can exist as a dimer or an octamer The dimeric and octameric forms are inter-changeable
  • 213. EMB-RCG CK-MT1 and CK-MT2 are encoded by different genes Thus, there are four genes for CK subunits These are CK-M, CK-B, CK-MT1 and CK- MT2
  • 214. EMB-RCG CK-M and CK-B genes encode the cytosolic enzyme CK-MT1 and CK-MT2 genes encode the mitochondrial enzyme CK-MT1 and CK-MT2 isoenzymes have no diagnostic importance
  • 215. EMB-RCG Bone, liver, intestine and placenta form different isoenzymes ALP isoenzymes are commonly separated by electrophoresis The liver isoenzyme moves the fastest It occupies the same position as a2-globulin Alkaline phosphatase
  • 216. EMB-RCG The bone ALP closely follows the liver ALP The placental isoenzyme follows the bone isoenzyme The intestinal isoenzyme is the slowest moving
  • 217. EMB-RCG The liver ALP is raised in liver cancer and biliary obstruction The bone ALP is raised in osteoblastic bone tumours and Paget’s disease The placental and intestinal isoenzymes have no diagnostic importance
  • 218. EMB-RCG Two atypical ALP isoenzymes are seen in some cancers These are Regan isoenzyme and Nagao isoenzyme These two resemble the placental isoenzyme
  • 219. EMB-RCG Regan isoenzyme is raised in cancer of breast, lungs, colon, uterus and ovaries Nagao isoenzyme is raised in germ cell cancer of the testes
  • 220. EMB-RCG Metabolic pathways need precise regulation Regulation ensures adequacy of products with no wastage of raw materials Requirements of the organism keep on changing Regulatory mechanisms must be responsive to these changes Regulation of enzymes
  • 221. Concentrations of enzymes Catalytic activity of enzymes Metabolic pathways are regulated by changing one of the following: Enzymes play a crucial role in the regulatory mechanisms
  • 222. The regulation involves one or a few “key” enzymes in a pathway EMB-RCG The rate-limiting step in the pathway The committed step in the pathway The key enzyme (or regulatory enzyme) may catalyse:
  • 223. EMB-RCG Rate-limiting step An early reaction that controls the availability of substrates for the subsequent reactions Committed step The earliest irreversible reaction unique to the pathway
  • 224. Regulation of enzyme concentration EMB-RCG Some pathways are regulated by changing the concentrations of the key enzymes The rates of reactions would change accordingly Concentration of an enzyme may be changed by altering its synthesis or its degradation Regulation of enzyme synthesis is commoner
  • 225. Regulation of enzyme synthesis EMB-RCG Enzyme synthesis may be regulated by: Induction of enzyme synthesis Repression of enzyme synthesis Conversion of proenzyme into enzyme
  • 226. EMB-RCG Enzymes may be divided into: Constitutive enzymes Inducible enzymes Induction
  • 228. EMB-RCG Inducer may be the substrate for the enzyme or may be a gratuitous inducer A gratuitous inducer is one which is not a substrate for the enzyme
  • 229. EMB-RCG The inducer acts on DNA, and increases the expression of the gene that encodes the enzyme An example is induction of key enzymes of gluconeogenesis by glucocorticoid hormones
  • 230. EMB-RCG Synthesis of some enzymes is regulated by repression Transcription of gene encoding the enzyme is blocked by a repressor The repressor is made up of apo-repressor and co-repressor Repression
  • 231. EMB-RCG Apo-repressor is a protein always present in the cell When co-repressor enters or accumulates in the cell, it combines with apo-repressor to form the repressor The co-repressor is generally the product of the pathway
  • 232. EMB-RCG An example is regulation of haem synthesis by d-aminolevulinic acid synthetase Haem acts as co-repressor, and represses the synthesis of this early enzyme in the pathway When the product is used up, the repression is relieved (derepression)
  • 233. Conversion of proenzyme into enzyme EMB-RCG Sometimes, the concentration of enzymes needs to be increased quickly For example, when food enters stomach, concentration of pepsin needs to be raised quickly This can not be done by induction or derepression which are slow processes
  • 234. EMB-RCG The enzyme is synthesized in the form of an precursor, pepsinogen Pepsinogen is an inactive proenzyme The proenzyme will not digest the mucosal proteins
  • 235. EMB-RCG Entry of food in the stomach generates some signals These signals convert pepsinogen into pepsin The enzyme concentration is raised quickly
  • 236. Proenzyme Enzyme Peptide Proteolysis Active site (masked) → Active site (exposed) → Proteolytic activation of proenzyme Substrate
  • 237. EMB-RCG Enzyme concentration may also be regulated by altering its breakdown Increased breakdown will decrease the concentration of the enzyme Decreased breakdown will increase the concentration of the enzyme Regulation of enzyme degradation
  • 238. EMB-RCG Regulation of degradation is not common in higher organisms A few examples are seen in starvation in which nutrients need to be conserved Concentration of some enzymes is increased by decreasing their breakdown An example of such enzyme is tryptophan pyrrolase
  • 239. EMB-RCG Regulation of catalytic activity of enzymes Enzyme concentration remains unchanged but its catalytic activity is altered The catalytic activity may be altered by: Allosteric regulation of the enzyme Covalent modification of the enzyme
  • 240. EMB-RCG Allosteric regulation This mechanism is used in some long metabolic pathways The substrate is converted into a product by a series of reactions The earliest functionally irreversible reaction is catalysed by an allosteric enzyme
  • 241. S I1 I2 I3 I4 P E1 E2 E3 E4 E5 EMB-RCG Usually, the product of the pathway is the allosteric inhibitor of the enzyme When the product accumulates, it inhibits the allosteric enzyme Θ
  • 242. EMB-RCG When the product is used up, the inhibition is relieved In this way, the rate of synthesis of product is regulated according to the rate of its utilisation If the pathway has a number of irreversible steps, regulation may occur at a number of steps
  • 243. EMB-RCG Some enzymes are regulated by positive allosteric modulation (activation) An example is regulation of carbamoyl phosphate synthetase I (mitochondrial) This enzyme is allosterically activated by N-acetylglutamate
  • 244. EMB-RCG Many enzymes are regulated by negative allosteric modulation (inhibition) An example is asparate transcarbamoylase It is an early enzyme in de novo synthesis of pyrimidine nucleotides It is inhibited by cytidine triphosphate, a product of the pathway
  • 245. EMB-RCG A few enzymes are subject to positive as well as negative allosteric regulation Phosphofructokinase-1, a regulatory enzyme in the glycolytic pathway, is subject to: Allosteric activation by AMP Allosteric inhibition by ATP
  • 246. Covalent modification EMB-RCG The enzymes regulated by this mechanism can exist in two forms These can be converted into each other by a covalent modification of the enzyme molecule The most common covalent modification is addition or removal of phosphate
  • 247. Phosphate is usually added to or removed from a serine residue in the enzyme A protein kinase adds phosphate, and a protein phosphatase removes phosphate P Protein kinase Protein phosphatase H2O ATP ADP Pi ENZYME‒Ser‒OH ENZYME‒Ser‒O‒ (Dephosphorylated enzyme) (Phosphorylated enzyme)
  • 248. EMB-RCG One form, either phosphorylated or dephospho- rylated, is active and the other is inactive Whether the enzyme is active or inactive depends upon the relative activities of protein kinase and protein phosphatase These, in turn, are controlled by hormones acting through second messengers
  • 249. EMB-RCG An example is glycogen synthetase ‒ active in the dephosphorylated form and inactive in the phosphorylated form Another example is glycogen phosphorylase ‒ inactive in the dephosphorylated form and active in the phosphorylated form
  • 250. For example, acetyl CoA carboxylase is subject to: Repression Allosteric regulation Covalent modification Induction Some enzymes are regulated by multiple mechanisms
  • 251. Assay of enzymes EMB-RCG Measurement of enzyme levels is often required for diagnostic/academic purposes Enzyme concentrations are very minute Isolation and purification of individual enzymes is laborious Therefore, direct measurement of enzyme concentrations is very difficult
  • 252. EMB-RCG Enzyme concentrations are measured indirectly Velocity of the enzyme-catalysed reaction is measured Conditions are such that rate of reaction is proportional to the enzyme concentration
  • 253. EMB-RCG To keep temperature constant, reaction is carried out in a fixed-temperature water-bath or incubator Optimum pH is maintained by using a buffer Substrate concentration is kept constant and high Under such conditions, rate of the reaction will be proportional to the enzyme concentration
  • 254. EMB-RCG The rate of the reaction can be determined by measuring: The rate of disappearance of the substrate Rate of appearance of the product
  • 255. EMB-RCG In endpoint methods: The reaction is carried out for a fixed period Initial and final concentrations of the substrate or the product are measured
  • 256. EMB-RCG In kinetic methods, the concentration of the substrate or the product is measured at regular intervals for a brief period The result in either case is expressed in arbitrary units of enzyme activity rather than enzyme concentration
  • 257. EMB-RCG Many enzymes are used as tools in diagnostic and research laboratories Glucose oxidase and peroxidase are used for measuring glucose concentration Hexokinase and glucose-6-phosphate dehydrogenase are also used for measuring glucose concentration Enzymes as laboratory tools
  • 258. EMB-RCG Cholesterol esterase, cholesterol oxidase and peroxidase are used for measuring cholesterol concentration Lipase, glycerol kinase, glycerol phosphate oxidase and peroxidase are used for measuring triglyceride concentration
  • 259. EMB-RCG Urease is used for measurement of urea concentration Uricase is used for measuring uric acid concentration Enzymes like peroxidase and alkaline phosphatase are used to label antibodies in ELISA
  • 260. EMB-RCG A number of enzymes are used in recombinant DNA technology e.g. Restriction endonuclease DNA ligase Terminal transferase S1 nuclease Reverse transcriptase Taq polymerase
  • 261. Enzymes as drugs EMB-RCG Some human, animal, plant and microbial enzymes are used as drugs also Digestive enzymes e.g. diastase, papain, pepsin, chymotrypsin etc are used to aid digestion Pancreatic amylase, lipase and proteases are used in the treatment of pancreatic insufficiency
  • 262. Serratiopeptidase is a bacterial proteolytic enzyme It is used to remove dead tissue from the site of inflammation to accelerate healing It is also used to reduce inflammation, oedema and pain
  • 263. Hyaluronidase catalyses hydrolysis of hyaluronic acid Hyaluronidase injections are used to facilitate delivery of other injectable drugs
  • 264. Asparaginase is used in the chemotherapy of leukaemia Leukaemic cells are deficient in asparagine synthetase They are dependent on pre-formed asparagine
  • 265. Asparaginase converts asparagine into aspartate This deprives the leukaemic cells of an essential nutrient
  • 266. EMB-RCG Thrombolytic drugs used to clear blockage of blood vessels are: Streptokinase Urokinase Tissue plasminogen activator